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研究生: 方森婭
Silvia Fontana
論文名稱: 紅火蟻的社會超級基因有許多基因和跳躍子上的拷貝數變異
The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
指導教授: 王忠信
John Wang
學位類別: 博士
Doctor
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2020
畢業學年度: 108
語文別: 英文
論文頁數: 114
中文關鍵詞: 紅火蟻超級基因社會染色體基因重覆跳躍子
英文關鍵詞: fire ant, supergene, social chromosome, gene duplication, transposons
DOI URL: http://doi.org/10.6345/NTNU202000202
論文種類: 學術論文
相關次數: 點閱:111下載:8
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  • The fire ant Solenopsis invicta shows two distinct social forms (monogyne and polygyne colonies, with one and multiple queens, respectively) under genetic control of a ~12.5 to 20 Mb supergene. The supergene includes ~600 genes linked together by multiple inversions, which prevents recombination between the two variants, ‘Social B’ (SB) and ‘Social b’ (Sb). In monogyne colonies all individuals carry only the SB allele, while in polygyne colonies, some individuals carry the Sb allele (all queens are heterozygotes SB/Sb, workers can be either SB/SB or SB/Sb and haploid males SB or Sb).
    In this study we characterized genes with copy number variation between SB and Sb-carrying individuals. We showed extensive acquisition of gene duplicates in the Sb genome, with some likely involved in polygyne-related phenotypes. We found 260 genes with copy number differences between SB and Sb, of which 239 have greater copy number in Sb.
    We observed transposable element (TE) accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. We found a weak correlation between TE copy number and differential expression, suggesting some TEs may still be proliferating in Sb while many of the duplicated TEs have already been silenced. Characterization of the TEs revealed showed the BEL family (LTR retrotransposons) was disproportionately duplicated in the supergene.
    While the presence of TEs in supergenes is well documented, little is known about duplication of non-TE genes and their possible adaptive role. Among the 115 non-TE genes with higher copy in Sb, we found genes with putative polygyne related functions, such as juvenile hormone synthesis, odorant reception, and innate immunity. Interestingly, enzymes responsible for cuticular hydrocarbon synthesis were highly represented.
    We identified candidate duplications, and conducted detailed examination of a desaturase and an elongase, as potentially responsible for different cuticular hydrocarbons profiles in SB/SB and SB/Sb queens. These genes, which are likely beneficial for polygyne ants and important for queen recognition, seem to have translocated into the supergene from other chromosomes and proliferated by multiple duplication events.
    Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.

    Acknowledgments i Abstract ii Table of Contents iv List of Tables vii List of Figures viii CHAPTER 1: Introduction 1 1.1. The fire ant Solenopsis invicta 1 1.2. Supergenes 3 1.3. Transposable elements (TEs) 4 1.4. Hypothesis 5 CHAPTER 2: Materials and Methods 8 2.1. Collection of transposable elements (TEs) and other fire ant genes to detect copy number variation (CNV) 8 2.1.1. Motivations 8 2.1.2. Trinity de novo assembly of 13 RNA-seq libraries for the collection of fire ant TEs 8 2.1.3. Collection of fire ant TEs 11 2.1.4. Collection of fire ant non-TE genes 12 2.1.5. Collection of TEs and other fire ant genes (nr-sinv-ref) to detect copy number variation (CNV) 12 2.2. Copy number variation (CNV) analysis 12 2.2.1. SB versus Sb whole genome sequencing reads 12 2.2.2. DNA read alignment to nr-sinv-ref 13 2.2.3. Copy number variation (CNV) analysis 14 2.3. Duplicated gene annotation and gene function over-representation analysis 15 2.4. DNA real-time quantitative PCR (qPCR) and digital droplet PCR (ddPCR) to detect copy number 16 2.4.1. Ant Sampling 16 2.4.2. DNA real-time quantitative PCR (qPCR): goals, primer design, and protocol 16 2.4.3. DNA digital droplet PCR (ddPCR): goals, primer design, and protocol 18 2.5. Gene expression of CNV genes 19 2.5.1. Differential expression (DE) analysis of CNV genes 19 2.5.2. Absolute expression analysis of CNV genes 21 2.6. Genomic analysis of CNV genes 21 2.6.1. Assembly and linkage group construction of SB and Sb genomes 21 2.6.2. Genomic analysis of CNV genes 22 2.6.3. Placement of SB contigs 000611F and 000344F onto chr 5 and chr 3, respectively 22 2.7. Analysis of desaturase and elongase copies 23 CHAPTER 3: Results 25 3.1. CNV analysis: duplicated TE and non-TE gene discovery 25 3.2. Validation of CNV results with quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR) 26 3.3. Higher transposon expression is weakly correlated to higher copy number 27 3.4. Enzymes involved in cuticular hydrocarbon (CHC) synthesis are highly duplicated in Sb and over-expressed in SB/Sb queens 29 3.5. CHC enzyme genes have copies on supergene and non-supergene chromosomes 31 3.6. Desaturase and elongase have potentially functional copies on Sb 32 CHAPTER 4: Discussion 34 4.1. TEs accumulation on Sb 34 4.2. Different functions of Non-TE genes with CNV between the Sb and SB fire ant genomes 37 4.3. CHC gene copies may have Sb functions 41 4.4. The role of TEs in gene duplication 44 CHAPTER 5: Conclusions 45 Tables 47 Figures 63 References 86 Appendices 98

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